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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtcaatcctttgctcctccatcccgacctcgtaaaagttccgcaacgccgtactgtcgctttccctgatcgcgtgttagttctctctctctctctgttcagGTACTGCGTCTGTTTCGACCCGCTGGATGGCTCCTCCAACATCGACTGTGGTGTCTCAATCGGAACG

Basic information

species Zea mays
transcript GRMZM2G322953_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G322953_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 3
-------------------gttcgtcaatcctttgctcctccatcccgacctcgtaa----aagttccgcaacgccgtactgtcgctttc-cctgatcgcgtgttagttctctctctctctctgttcagGTACTGCGTCTGTTTCGACCCGCTGGATGGCTCCTCCAACATCGACTGTGGTGTCTCAATCGGAACG
                   || |  | | | | | || |||  |  | | ||   |      |||||  |||   | |  || |  ||||  || |||    | | |  |    || || ||| |||||||| ||||| ||||| || || |||||||||||||| || ||||| ||||||||||| ||||| |||
gtatgtgaaatttatgatagtactactaccatgttcttctcagttgctagctatcagccacgagttcgacaagatcatggtgactgtttcgtctcatcagaagct-gcacgggttccctttctcttcagGTATTGCGTTTGTTTTGATCCACTGGATGGCTCCTCAAATATCGATTGTGGTGTCTCCATCGGGACG

upper sequence: GRMZM2G322953_T04 (Zea mays), 3'ss of exon 3
lower sequence: EFJ04554 (Selaginella moellendorffii), 3'ss of exon 4
gttcgtcaatcctttgctcctccatcccgacctcgtaaaagttccgcaacgccgtactgtcgctttccctgatcgcgtgttagttctctctctctctctgttcagGTACTGCGTCTGTTTCGACCCGCTGGATGGCTCCTCCAACATCGACTGTGGTGTCTCAATCGGAACG
                                                     |||      || |  || |      | || |||| |      ||    | || ||||| ||   ||| || || ||||||||||| || |||||||||||||||||||| || ||||| 
-----------------------------------------------------gtaagtaaactataactcaaacgtcgctaattcttttctcgactgatcttagATACTGTGTGGTTTTTGATCCTCTGGATGGCTCGTCTAACATCGACTGTGGTGTCTCGATTGGAACT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211164076|gb|FL013514.1|FL013514
EST:     TCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCCCTCCGCGGGAA                         GTACTGCGTCTGTTTCGACCCGCTGGATGGCTCCTC
genomic: TCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCCCTCCGCGGGAAgttcgtcaat ... ctctgttcagGTACTGCGTCTGTTTCGACCCGCTGGATGGCTCCTC
EST: gi|211164067|gb|FL013505.1|FL013505
EST:     TCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCCCTCCGCGGGAA                         GTACTGCGTCTGTTTCGACCCGCTGGATGGCTCCTCCAACATCGACTGTGG
genomic: TCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCCCTCCGCGGGAAgttcgtcaat ... ctctgttcagGTACTGCGTCTGTTTCGACCCGCTGGATGGCTCCTCCAACATCGACTGTGG
EST: gi|211164074|gb|FL013512.1|FL013512
EST:     TCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCCCTCCGCGGGAA                         GTACTGCGTCTGTTTCGACCCGCTGGATGGCTCCTCCAACATCGACTGTGG
genomic: TCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCCCTCCGCGGGAAgttcgtcaat ... ctctgttcagGTACTGCGTCTGTTTCGACCCGCTGGATGGCTCCTCCAACATCGACTGTGG
EST: gi|211164075|gb|FL013513.1|FL013513
EST:     CTGAAGAGAACGAGGAGGNCATCTTCGTCGACCCGGCCCTCCCGCGG-AA                         GTACTGCGTCTGTTTCGACCCGCTGGATGGGTCCTCCCACATCGACTGTG
genomic: CTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCCCTCC-GCGGGAAgttcgtcaat ... ctctgttcagGTACTGCGTCTGTTTCGACCCGCTGGATGGCTCCTCCAACATCGACTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgtactgtcgctttccctgatcgcgtgttagttctctctctctctctgttcagGTACTGCGTCTGTTTCGACCCGCTGGATGGCTCCTCCAACATCGACTGTGGTGTCTCAATCGGAACG
                ccctgat  putative branch site (score: 4)
                             ttagttctctctctct  putative PPT
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtcaatcctttgctcctccatcccgacctcgtaaaagttccgcaacgccgtactgtcgctttccctgatcgcgtgttagttctctctctctctctgttcagGTACTGCGTCTGTTTCGACCCGCTGGATGGCTCCTCCAACATCGACTGTGGTGTCTCAATCGGAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC